The discovery of the variant could help doctors find those people at high risk of severe flu and prioritize them for treatment, researchers said.
It may also help explain why new strains of flu virus often emerge first in Asia, where the variant known as rs12252-C is more common in the population than elsewhere, they said.
"Understanding why some people may be worse affected than others is crucial in improving our ability to manage flu epidemics and to prevent people dying from the virus," said Tao Dong at Britain's Oxford University, who led the study.
The research, published in the journal Nature Communications on Tuesday, found that having the rs12252-C variant could increase the chances of severe infection by six times.
H1N1 swine flu swept around the world in 2009 and 2010. A study published last week estimated at least one in five people worldwide were infected and around 200,000 killed in the first year of the outbreak, which was declared a pandemic by the World Health Organisation in June 2009.
Previous research has found that rs12252-C is linked to more severe flu infections.
For this study, researchers focused on the variant because it is 100 times more common in Han Chinese, the predominant ethnic group in China, than in Caucasian populations indigenous to West Asia and Europe. The variant is present in the genetic make-up of about 1 in 3,000 people in Caucasian populations.
The results showed it was present in 69 percent of Chinese patients with severe pandemic H1N1 in 2009 compared with 25 percent who only had a mild version of the infection.
Andrew McMichael of Oxford's human immunology unit said further studies are now needed to look in more detail at the gene variant's effect on flu severity in different populations.
"It remains to be seen how this gene affects the whole picture of influenza in China and South East Asia but it might help explain why new influenza viruses often first appear in this region of the world," he said in a statement.
(Reporting by Kate Kelland; Editing by Tom Pfeiffer)